[gmx-users] grompp error in peptide-membrane simulations

[maite lopez]

Hi Tsjerk:

thanks again for the full description of what i should to do.
I did it and grompp runs !!!!!

cheers

Maite



On 3/3/07, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
Hi Maite,
>
> Indeed you shouldn't really run the lipids through pdb2gmx, but try to
> obtain a .itp file for a lipid, matching the force field you're trying
> to use. What you can do is take one lipid and run it through pdb2gmx,
> using your favourite force field. Make sure that the resulting
> structure file is not different in terms of the number of atoms and
> the order of them. Then you can use #include "lipid_ffG53a5.itp" in
> your .top file and under system list the number of lipids you have in
> your structure file. It may be a good idea to edit the
> lipid_ff53a6.itp file and change the name of the molecule. I hope I'm
> a bit clear, but in case I'm not, I think that you have to do
> additional reading of the manual in order to understand the topology
> files (chapter 5) until you grasp the idea. Now, to summarize a bit:
>
> 1. Construct the topology for your protein using pdb2gmx+ffG53a5
> 2. Extract one lipid from lipid.pdb and run it through pdb2gmx+ffG53a5
> 3. Modify the resulting .top file from #2 to make it a .itp file (a
> molecule definition)
> 4. Set up the system consisting of the protein and the lipids (and
> make sure that all the lipids are whole, i.e. not split over the
> periodic boundaries)
> 5. construct the topology for the system by adding the lipid topology
> to the protein.top file.
>
> Hope it helps,
>
> Tsjerk
>
>
> On 3/3/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> > maite lopez wrote:
> >
> > > i've changed the atoms of the dppc.itp  file by the atoms of the DPPC
> > > molecule that appear in the ffG53a5.rtp file (for example LC3 by CH3)
> > > and run grompp , but it gives :
> > > Fatal error:
> > > Atomtype 'C1' not found!
> > >
> > > I don´t  know  how  to convert my  lipids to ffG53a5. Could you
> > > explain me briefly?
> >
> > So find where C1 is being referenced, and whether it should be being
> > defined elsewhere, and if it isn't defined work out why it isn't.
> >
> > Mark
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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